Transcriptome analysis by pyrosequencing: A new tool for assessing the response of marine animals to environmental stress

SHARE THIS:

Sibel I. Karchner, Biology
Mark E. Hahn, Biology

Grant Funded 2008

Marine organisms are continually challenged by changing environmental
conditions, including wide variations in temperature, pressure,
salinity, oxygen tension, light, nutrient availability, or the
concentrations of toxic chemicals (natural or anthropogenic). They
respond to this variable environment in large part through changes in
gene expression, which underlie adaptive physiological capabilities
that serve to mitigate the environmental stress. Study of these
adaptive changes in terrestrial and laboratory model organisms has been
facilitated by the increasing number of sequenced genomes of these
organisms, and the associated microarray resources for performing gene
expression profiling. However, for the vast majority of marine
organisms—and marine animals in particular—such resources are lacking.
For non-model organisms without sequenced genomes, current approaches
for measuring altered gene expression on a genome-scale are inadequate
or prohibitively expensive.

Recently, the “next generation” of DNA sequencing technologies has
increased the throughput and reduced the cost of DNA sequencing by
orders of magnitude. The method of pyrosequencing on high-density
picoliter plates pioneered by 454 Life Sciences (now Roche Applied
Sciences) combines high-throughput (400,000 individual sequences per
run) with long reads (currently ~250 bp, soon to be 400 bp) and high
accuracy. We propose to conduct experiments that will provide proof of
concept regarding the application of 454 pyrosequencing to studies of
gene expression in response to environmental stress in marine
metazoans. To do this, we will characterize the transcriptome of the
Atlantic killifish (mummichog) (Fundulus heteroclitus) and
measure the transcriptional response to environmental stresses, using
hypoxia and toxic chemicals as examples. These studies will be the
first application of pyrosequencing technology to combine transcriptome
characterization and gene expression profiling in a marine metazoan.
The pyrosequencing approach has great potential for application to a
variety of problems in marine science, including studies in ecology,
evolution, population biology, life history transitions, and adaptation
to extreme and variable environments.

The Woods Hole Oceanographic Institution is dedicated to research and education to advance understanding of the ocean and its interaction with the Earth system, and to communicating this understanding for the benefit of society. Learn more »